The test HelpSupportTestCase#testStandalone is flaky because it calls SynopsisGenerator which uses a HashSet as its data structure for the conflicts object. When comparing the conflicts object with the expected test results with assertEquals the test is flaky as HashSet does not maintain order. Fix: changed the conflicts and conflicts2 objects from HashSet to LinkedHashSet in method SynopsisGenerator#addSynopsisOption(SynopsisOption).

The test BootScriptInvokerTestCase is flaky becauses it uses a HashSet as its data structure for the echos object. When comparing the echos object with the expected test results with assertEquals the test is flaky as HashSet does not maintain order. Fix: changed the echos object from HashSet to LinkedHashSet in method.